nf-core_modules/modules/sequenzautils/bam2seqz/meta.yml
Kevin 3aacd46da2
Backfill software licenses meta (#876)
* backfilled modules with meta.yml that had no license identifier

* harmonized BSD license names

* whitespace linting at modules/unzip/meta.yml:12

* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'

* Update modules/bcftools/index/meta.yml

`bcftools` is dual-licensed, use associative array to allow for multiple licenses

Co-authored-by: Michael L Heuer <heuermh@acm.org>

Co-authored-by: Michael L Heuer <heuermh@acm.org>
2021-10-22 15:39:54 -07:00

50 lines
1.7 KiB
YAML
Executable file

name: sequenzautils_bam2seqz
description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
keywords:
- bam2seqz
tools:
- sequenzautils:
description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
doi: 10.1093/annonc/mdu479
licence: ['GPL-3.0-or-later']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- normalbam:
type: file
description: BAM file from the reference/normal sample
pattern: "*.{bam}"
- tumourbam:
type: file
description: BAM file from the tumour sample
pattern: "*.{bam}"
- fasta:
type: file
description: Reference FASTA file
pattern: "*.{fasta}"
- wigfile:
type: file
description: GC content wiggle file
pattern: "*.{wig.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- seqz:
type: file
description: Seqz file
pattern: "*.{seqz.gz}"
authors:
- "@kaurravneet4123"